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Crystal structure of ubiquitin-like domain of human WDR12

Analyse Crystal structure of ubiquitin-like domain of human WDR12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6P0Q
Type: protein
Length: 186 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosome biogenesis protein WDR12
UniProt: Q9GZL7
Pockets: 2 · best druggability 0.31

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribosome biogenesis protein WDR12	protein	93	27% helix, 25% strand	Q9GZL7

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 5 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	64	0.31	0.75	13	empty
2	52	0.27	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 876 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6P0Q · Crystal Structure of Ubiquitin-like Domain of Human WDR12 · the same entry in another collection · chain A against A, TM-score 1.00
Q9GZL7 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein WDR12 (Q9GZL7) · a predicted model of the same protein · chain A against A, TM-score 0.94

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9GZL7
Elsewhere: RCSB PDB 6P0Q · PDBe 6P0Q · UniProt Q9GZL7

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